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Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/Hong Kong/1/68 (h3n2) with bound m7GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQZ PDB ENTRY 2VQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2M lithium nitrate, 0.1M Tris-HCl pH 8.0, 18% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.379 α = 90 b = 70.151 β = 90 c = 93.941 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 30 91.7 11.9 12525 12525
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VQZ 1.95 28.26 12491 11879 612 91.48 0.2276 0.18656 0.18349 0.1812 0.24627 0.2441 RANDOM 43.353
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.23 0.18 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.079 r_dihedral_angle_3_deg 17.847 r_dihedral_angle_4_deg 16.735 r_sphericity_free 7.952 r_dihedral_angle_1_deg 6.8 r_scangle_it 6.111 r_sphericity_bonded 4.376 r_scbond_it 3.973 r_mcangle_it 2.703 r_rigid_bond_restr 2.588
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.079 r_dihedral_angle_3_deg 17.847 r_dihedral_angle_4_deg 16.735 r_sphericity_free 7.952 r_dihedral_angle_1_deg 6.8 r_scangle_it 6.111 r_sphericity_bonded 4.376 r_scbond_it 3.973 r_mcangle_it 2.703 r_rigid_bond_restr 2.588 r_angle_refined_deg 2.258 r_mcbond_it 1.664 r_chiral_restr 0.161 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1293 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 37
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling